I just rebuild me engine, put it back in and got it running, but now the Jeep won't drive.

I can hear the big 'clonk' as she goes into R or Low 1. I checked the vacuum lines and found the rubber had split and snapped off by the control mechanism on the transfer case.
I put new hoses on and can feel vacuum, but she won't lock and drive. Two weeks ago when I was driving her, I had no problems.

Could the diaphram have gone all of a sudden?

I have a 76 Chief as a spares car which also has a QT, however I notice that there are only two vacuum lines at the transfer case end, where my 78 has three. The third runs to another vacuum source on the manifold, in addition to the glove box switch vacuum source.

Is this normal does anyone know?

Also has anyone tried and tested a mechanical switch. I don't mind crawling under the car to lock the transfer case - I would much rather that, than be at the mercy of some vacuum pipe and a diaphram in the middle of nowwhere, 100 miles from water!

You should have one small vacuum line coming from the engine to the switch, 2 small vacuum lines from the switch to the tcase. The other line off the tcase should be the vent, as lucdog said, ad much larger than the lines from the switch.

The clunk is normal (not so much good, but normal) and should be tranny engaging tcase.

If qtrac is not moving jeep at all, I would guess what lucdog said, that you have the low-range, and it's in neutral. Down is hi, up is lo. When putting mine into hi, half the time the handle hits the floor, and I think I'm i hi until I try to move, and nothing happens.

As far as being stuck, it only uses the vacuum for the switching, not to hold it locked or unlocked. So, you can run vacuum to one of the spots on the tcase, locking it in, and then take it off, drive out, and hook it to the other to unlock.

http://www.mityvac.com/pages/products_bcbe.asp
Just hook a line from the actuator to it and pump up some vacuum. You should then hear the actuator move, then connect the line to the other side and repeat.
The plus by doing it this way is no engine noise.